drake_md_report

HYPOTHESES

C amendments will increase diversity of SOM molecules
C amendments will cause a depletion of aromatic molecules, especially in fine pores
Homogenization will increase (a) total peaks, (b) diversity of peaks, (c) aromatic peaks

We selected only peaks seen in >1 of the 4 replicates (i.e. n = 2 or 3 or 4)

setup

how many FTICR reps per treatment type?

click to open

SampleAssignment	reps
50-drought-groundw-control-Intact	2
50-drought-precip-C-Intact	2
1.5-drought-groundw-C-Homogenized	3
1.5-drought-groundw-C-Intact	3
1.5-drought-groundw-control-Homogenized	3
1.5-drought-groundw-N-Intact	3
1.5-drought-precip-C-Homogenized	3
1.5-drought-precip-N-Homogenized	3
1.5-fm-precip-C-Intact	3
1.5-fm-precip-N-Homogenized	3
50-drought-groundw-control-Homogenized	3
50-drought-groundw-N-Intact	3
50-drought-precip-control-Homogenized	3
50-fm-groundw-control-Intact	3
50-fm-groundw-N-Homogenized	3
50-fm-precip-control-Homogenized	3
50-fm-precip-N-Homogenized	3
1.5-drought-groundw-control-Intact	4
1.5-drought-groundw-N-Homogenized	4
1.5-drought-precip-C-Intact	4
1.5-drought-precip-control-Homogenized	4
1.5-drought-precip-control-Intact	4
1.5-drought-precip-N-Intact	4
1.5-fm-groundw-C-Homogenized	4
1.5-fm-groundw-C-Intact	4
1.5-fm-groundw-control-Homogenized	4
1.5-fm-groundw-control-Intact	4
1.5-fm-groundw-N-Homogenized	4
1.5-fm-groundw-N-Intact	4
1.5-fm-precip-C-Homogenized	4
1.5-fm-precip-control-Homogenized	4
1.5-fm-precip-control-Intact	4
1.5-fm-precip-N-Intact	4
50-drought-groundw-C-Homogenized	4
50-drought-groundw-C-Intact	4
50-drought-groundw-N-Homogenized	4
50-drought-precip-C-Homogenized	4
50-drought-precip-control-Intact	4
50-drought-precip-N-Homogenized	4
50-drought-precip-N-Intact	4
50-fm-groundw-C-Homogenized	4
50-fm-groundw-C-Intact	4
50-fm-groundw-control-Homogenized	4
50-fm-groundw-N-Intact	4
50-fm-precip-C-Homogenized	4
50-fm-precip-C-Intact	4
50-fm-precip-control-Intact	4
50-fm-precip-N-Intact	4

so we select formulae seen in at least 2 reps per treatment type

van krevelens

domains, baseline

fticr domains

VK by replication

VK by treatment

VK diagrams by treatment

VK unique

unique to each amendment, in each incubation type

peaks

graphs

total peaks

complex:simple compounds

peak count tables

tables – total peaks

Homogenization	Moisture	Wetting	1.5-control	1.5-C	1.5-N	50-control	50-C	50-N
Intact	drought	groundw	736 ± 180	1598 ± 180	913 ± 381	884 ± 0	2155 ± 663	802 ± 70
Intact	drought	precip	1008 ± 274	1857 ± 208	1326 ± 49	1768 ± 194	2823 ± 0	1567 ± 129
Intact	fm	groundw	915 ± 124	698 ± 34	848 ± 196	1144 ± 273	1064 ± 137	1036 ± 201
Intact	fm	precip	596 ± 89	637 ± 61	497 ± 80	1181 ± 276	3149 ± 272	1423 ± 47
Homogenized	drought	groundw	2411 ± 136	1863 ± 245	1394 ± 221	2149 ± 205	3294 ± 290	992 ± 227
Homogenized	drought	precip	1121 ± 391	1089 ± 109	1227 ± 151	1261 ± 173	1576 ± 701	1829 ± 584
Homogenized	fm	groundw	933 ± 134	899 ± 176	490 ± 47	2475 ± 455	1408 ± 175	568 ± 119
Homogenized	fm	precip	1475 ± 209	609 ± 162	804 ± 129	2208 ± 141	3689 ± 339	844 ± 255

tables – complex peaks

Homogenization	Moisture	Wetting	1.5-control	1.5-C	1.5-N	50-control	50-C	50-N
Intact	drought	groundw	520 ± 143	1159 ± 181	583 ± 241	778 ± 0	1609 ± 507	594 ± 61
Intact	drought	precip	733 ± 204	1220 ± 136	977 ± 25	1469 ± 158	2109 ± 0	1148 ± 87
Intact	fm	groundw	590 ± 93	431 ± 16	442 ± 81	894 ± 233	689 ± 79	747 ± 166
Intact	fm	precip	374 ± 64	439 ± 51	345 ± 62	905 ± 207	2341 ± 175	1039 ± 43
Homogenized	drought	groundw	2175 ± 121	1535 ± 227	1030 ± 187	1767 ± 215	2818 ± 233	774 ± 204
Homogenized	drought	precip	889 ± 317	825 ± 90	978 ± 133	1045 ± 162	1396 ± 667	1488 ± 506
Homogenized	fm	groundw	677 ± 94	557 ± 120	331 ± 32	2094 ± 453	1065 ± 178	425 ± 79
Homogenized	fm	precip	1007 ± 100	379 ± 107	557 ± 106	1605 ± 95	3229 ± 285	687 ± 229

relative abundances

relative abundance of complex peaks

STATS

PERMANOVA

overall

#> 
#> Call:
#> adonis(formula = relabund_wide %>% select(aliphatic:condensed_arom) ~      (Amendments + Moisture + Wetting + Suction + Homogenization)^3,      data = relabund_wide) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                                     Df SumsOfSqs MeanSqs F.Model      R2
#> Amendments                           2   0.14437 0.07219   7.811 0.04766
#> Moisture                             1   0.21505 0.21505  23.270 0.07099
#> Wetting                              1   0.00916 0.00916   0.991 0.00302
#> Suction                              1   0.38447 0.38447  41.602 0.12691
#> Homogenization                       1   0.17475 0.17475  18.909 0.05768
#> Amendments:Moisture                  2   0.04268 0.02134   2.309 0.01409
#> Amendments:Wetting                   2   0.05754 0.02877   3.113 0.01899
#> Amendments:Suction                   2   0.02715 0.01357   1.469 0.00896
#> Amendments:Homogenization            2   0.13898 0.06949   7.519 0.04588
#> Moisture:Wetting                     1   0.01834 0.01834   1.985 0.00606
#> Moisture:Suction                     1   0.05683 0.05683   6.149 0.01876
#> Moisture:Homogenization              1   0.00560 0.00560   0.606 0.00185
#> Wetting:Suction                      1   0.04302 0.04302   4.655 0.01420
#> Wetting:Homogenization               1   0.05849 0.05849   6.329 0.01931
#> Suction:Homogenization               1   0.02368 0.02368   2.562 0.00782
#> Amendments:Moisture:Wetting          2   0.08926 0.04463   4.829 0.02946
#> Amendments:Moisture:Suction          2   0.03187 0.01593   1.724 0.01052
#> Amendments:Moisture:Homogenization   2   0.04422 0.02211   2.392 0.01460
#> Amendments:Wetting:Suction           2   0.03512 0.01756   1.900 0.01159
#> Amendments:Wetting:Homogenization    2   0.02055 0.01027   1.112 0.00678
#> Amendments:Suction:Homogenization    2   0.08361 0.04181   4.524 0.02760
#> Moisture:Wetting:Suction             1   0.02044 0.02044   2.212 0.00675
#> Moisture:Wetting:Homogenization      1   0.00995 0.00995   1.077 0.00328
#> Moisture:Suction:Homogenization      1   0.02605 0.02605   2.819 0.00860
#> Wetting:Suction:Homogenization       1   0.01140 0.01140   1.233 0.00376
#> Residuals                          136   1.25687 0.00924         0.41488
#> Total                              172   3.02945                 1.00000
#>                                    Pr(>F)    
#> Amendments                          0.001 ***
#> Moisture                            0.001 ***
#> Wetting                             0.368    
#> Suction                             0.001 ***
#> Homogenization                      0.001 ***
#> Amendments:Moisture                 0.052 .  
#> Amendments:Wetting                  0.017 *  
#> Amendments:Suction                  0.191    
#> Amendments:Homogenization           0.001 ***
#> Moisture:Wetting                    0.159    
#> Moisture:Suction                    0.004 ** 
#> Moisture:Homogenization             0.586    
#> Wetting:Suction                     0.015 *  
#> Wetting:Homogenization              0.005 ** 
#> Suction:Homogenization              0.073 .  
#> Amendments:Moisture:Wetting         0.001 ***
#> Amendments:Moisture:Suction         0.145    
#> Amendments:Moisture:Homogenization  0.058 .  
#> Amendments:Wetting:Suction          0.096 .  
#> Amendments:Wetting:Homogenization   0.347    
#> Amendments:Suction:Homogenization   0.004 ** 
#> Moisture:Wetting:Suction            0.124    
#> Moisture:Wetting:Homogenization     0.329    
#> Moisture:Suction:Homogenization     0.079 .  
#> Wetting:Suction:Homogenization      0.294    
#> Residuals                                    
#> Total                                        
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

PERMANOVA for treatments

1.5 kPa intact cores

#> 
#> Call:
#> adonis(formula = intact_1_5 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = intact_1_5) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.00603 0.003014  0.4995 0.01288  0.754    
#> Moisture                     1   0.07530 0.075298 12.4784 0.16088  0.001 ***
#> Wetting                      1   0.05498 0.054976  9.1107 0.11746  0.001 ***
#> Amendments:Moisture          2   0.02583 0.012913  2.1399 0.05518  0.079 .  
#> Amendments:Wetting           2   0.04222 0.021109  3.4981 0.09020  0.017 *  
#> Moisture:Wetting             1   0.01142 0.011423  1.8931 0.02441  0.136    
#> Amendments:Moisture:Wetting  2   0.05315 0.026576  4.4042 0.11356  0.006 ** 
#> Residuals                   33   0.19913 0.006034         0.42545           
#> Total                       44   0.46805                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

50 kPa intact cores

#> 
#> Call:
#> adonis(formula = intact_50 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = intact_50) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.08850 0.044252  5.8702 0.19694  0.001 ***
#> Moisture                     1   0.01117 0.011168  1.4815 0.02485  0.237    
#> Wetting                      1   0.01314 0.013136  1.7426 0.02923  0.181    
#> Amendments:Moisture          2   0.03599 0.017997  2.3875 0.08010  0.058 .  
#> Amendments:Wetting           2   0.02278 0.011392  1.5112 0.05070  0.222    
#> Moisture:Wetting             1   0.02859 0.028587  3.7923 0.06361  0.029 *  
#> Amendments:Moisture:Wetting  2   0.02308 0.011538  1.5305 0.05135  0.225    
#> Residuals                   30   0.22615 0.007538         0.50323           
#> Total                       41   0.44940                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

1.5 kPa homogenized cores

#> 
#> Call:
#> adonis(formula = homo_1_5 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = homo_1_5) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.11805 0.059026  7.9299 0.16791  0.001 ***
#> Moisture                     1   0.20467 0.204672 27.4967 0.29111  0.001 ***
#> Wetting                      1   0.01808 0.018077  2.4286 0.02571  0.078 .  
#> Amendments:Moisture          2   0.02850 0.014249  1.9143 0.04053  0.112    
#> Amendments:Wetting           2   0.03984 0.019918  2.6758 0.05666  0.046 *  
#> Moisture:Wetting             1   0.01283 0.012831  1.7238 0.01825  0.164    
#> Amendments:Moisture:Wetting  2   0.05037 0.025186  3.3836 0.07164  0.021 *  
#> Residuals                   31   0.23075 0.007443         0.32819           
#> Total                       42   0.70308                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

50 kPa homogenized cores

#> 
#> Call:
#> adonis(formula = homo_50 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = homo_50) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.19013 0.095065  6.7194 0.22768  0.001 ***
#> Moisture                     1   0.00599 0.005993  0.4236 0.00718  0.670    
#> Wetting                      1   0.03243 0.032430  2.2922 0.03884  0.128    
#> Amendments:Moisture          2   0.07244 0.036221  2.5602 0.08675  0.047 *  
#> Amendments:Wetting           2   0.03066 0.015328  1.0835 0.03671  0.401    
#> Moisture:Wetting             1   0.00933 0.009327  0.6593 0.01117  0.534    
#> Amendments:Moisture:Wetting  2   0.05551 0.027754  1.9617 0.06647  0.099 .  
#> Residuals                   31   0.43858 0.014148         0.52520           
#> Total                       42   0.83506                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

PCA

overall PCA

PCA individual treatments

individual cores

others

other plots

NOSC

elements

Session Info

click to expand

Date run: 2020-08-17

#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#> 
#> Matrix products: default
#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] lme4_1.1-23      Matrix_1.2-18    car_3.0-9        carData_3.0-4   
#>  [5] visNetwork_2.0.9 vegan_2.5-6      lattice_0.20-41  permute_0.9-5   
#>  [9] rmarkdown_2.3    drake_7.12.4     ggbiplot_0.55    PNWColors_0.1.0 
#> [13] forcats_0.5.0    stringr_1.4.0    dplyr_1.0.1      purrr_0.3.4     
#> [17] readr_1.3.1      tidyr_1.1.1      tibble_3.0.3     ggplot2_3.3.2   
#> [21] tidyverse_1.3.0  here_0.1        
#> 
#> loaded via a namespace (and not attached):
#>  [1] minqa_1.2.4        colorspace_1.4-1   ellipsis_0.3.1    
#>  [4] rio_0.5.16         rprojroot_1.3-2    fs_1.5.0          
#>  [7] rstudioapi_0.11    farver_2.0.3       soilpalettes_0.1.0
#> [10] fansi_0.4.1        lubridate_1.7.9    xml2_1.3.2        
#> [13] splines_4.0.2      knitr_1.29         jsonlite_1.7.0    
#> [16] nloptr_1.2.2.2     packrat_0.5.0      broom_0.7.0       
#> [19] cluster_2.1.0      dbplyr_1.4.4       shiny_1.5.0       
#> [22] compiler_4.0.2     httr_1.4.2         backports_1.1.8   
#> [25] assertthat_0.2.1   fastmap_1.0.1      cli_2.0.2         
#> [28] later_1.1.0.1      htmltools_0.5.0    prettyunits_1.1.1 
#> [31] tools_4.0.2        igraph_1.2.5       gtable_0.3.0      
#> [34] agricolae_1.3-3    glue_1.4.1         tinytex_0.25      
#> [37] Rcpp_1.0.5         cellranger_1.1.0   vctrs_0.3.2       
#> [40] nlme_3.1-148       xfun_0.16          openxlsx_4.1.5    
#> [43] rvest_0.3.6        mime_0.9           miniUI_0.1.1.1    
#> [46] lifecycle_0.2.0    statmod_1.4.34     MASS_7.3-51.6     
#> [49] scales_1.1.1       hms_0.5.3          promises_1.1.1    
#> [52] parallel_4.0.2     yaml_2.2.1         curl_4.3          
#> [55] labelled_2.5.0     stringi_1.4.6      highr_0.8         
#> [58] klaR_0.6-15        AlgDesign_1.2.0    filelock_1.0.2    
#> [61] boot_1.3-25        zip_2.1.0          storr_1.2.1       
#> [64] rlang_0.4.7        pkgconfig_2.0.3    evaluate_0.14     
#> [67] labeling_0.3       htmlwidgets_1.5.1  tidyselect_1.1.0  
#> [70] plyr_1.8.6         magrittr_1.5       R6_2.4.1          
#> [73] generics_0.0.2     base64url_1.4      combinat_0.0-8    
#> [76] txtq_0.2.3         DBI_1.1.0          pillar_1.4.6      
#> [79] haven_2.3.1        foreign_0.8-80     withr_2.2.0       
#> [82] mgcv_1.8-31        abind_1.4-5        modelr_0.1.8      
#> [85] crayon_1.3.4       questionr_0.7.1    progress_1.2.2    
#> [88] grid_4.0.2         readxl_1.3.1       data.table_1.13.0 
#> [91] blob_1.2.1         reprex_0.3.0       digest_0.6.25     
#> [94] xtable_1.8-4       httpuv_1.5.4       munsell_0.5.0